long-read sequencing

Somatic Structural Variant Discovery from Tumor Specific Strings Computed Against a Draft Composite Germline Reference

VESPA-SS detects somatic structural variants from long-read sequencing data without requiring read mapping or a high-quality germline reference, achieving high F1 scores on cancer cell lines.

spearfish: ultrafast Δ-mapping of long reads to redundant transcriptomes

spearfish improves long-read mapping efficiency by leveraging transcriptome redundancy, achieving faster speeds and lower memory usage than existing tools.

Towards a foundation model for raw nanopore signal through discrete tokenization

This paper introduces Brieno, a self-supervised model for raw nanopore signals that improves read classification and methylation detection without reference genomes.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.

SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

SQANTI-evidence annotates genomes from long-read RNA-seq without a reference, achieving high precision in gene and isoform prediction across species.

Transcript quantification using context-aware MAPQ modeling

CALMeR improves transcript quantification by context-aware MAPQ modeling, recovering more spike-in transcripts and better matching known concentrations.

mito-overview: a mitochondrial report software

mito-overview integrates mitochondrial coverage, allele fractions, annotations, and read co-occurrence to identify and analyze candidate variants in mitochondrial genomic reports.

ONT-LibQC: rapid quality control of chromatin assay libraries using shallow nanopore sequencing

ONT-LibQC uses shallow nanopore sequencing to rapidly assess chromatin assay library quality before deep sequencing, showing consistent results with Illumina sequencing.

T2G: fast and accurate transcriptome to genome BAM liftover for short and long read RNA sequencing

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

Accurate repeat expansion genotyping from whole-genome and real-time targeted nanopore sequencing with Mahi-mahi

Mahi-mahi accurately genotypes repeat expansions from nanopore sequencing data, matching orthogonal methods and identifying pathogenic alleles.

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Modulator processes nanopore direct-RNA sequencing data to differentiate transcript-, allele-, and condition-associated RNA modifications, improving the analysis of RNA modifications in single molecules.

SLAFIT: Viral fitness inference and structural variant detection from TGS data

SLAFIT infers viral fitness and detects structural variants from third-generation sequencing data by analyzing linkage disequilibrium and haplotype frequencies.

DIPLER: rapid k-mer-based locus identification

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.

DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family

DUMMEST improves frameshift-aware alignment of DNA sequences to protein families by combining simplicity and speed, outperforming existing methods in sensitivity and specificity.

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

The Genetic Landscape of Structural Variants in Aspergillus flavus using ONT and PacBio Sequencing

This study uses long-read sequencing to analyze structural variants in Aspergillus flavus, identifying homopolymer tracts and deletions that arise spontaneously.

A novel analysis pipeline and experimental design for measuring expanded repeat instability

Delta plots from targeted long-read data separate repeat instability frequency, expansion bias and change size; a single-clone assay (SCIA) shows FAN1 knockout raises expansion frequency but shrinks expansions.

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

Long-read sequencing reveals genomic landscape of structural variants in a major disease vector

The paper uses long-read sequencing to identify structural variants in Culex quinquefasciatus, revealing their potential role in insecticide resistance and adaptation.

Long-read sequencing with targeted assembly of the opsin locus accurately evaluates genes in expressed positions

This paper evaluates long-read sequencing with targeted assembly for accurately analyzing the opsin gene cluster, showing high concordance and improved detection of color vision deficiencies and carrier status.

A reference genome without a virus: cDNA reconstruction reveals the provenance and function of the MS2 phage sequence

The paper reconstructs the MS2 phage genome using cDNA and shows that the current NCBI reference genome does not produce infectious phage, highlighting the need to verify reference genome infectivity.

Nailpolish: Reference-free UMI deduplication and consensus read generation

Nailpolish reduces error rates and improves deduplication of UMI-tagged long reads across multiple sequencing technologies and protocols.

Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq

PICARD-seq enables rapid, affordable whole-plasmid sequencing using nanopore technology, improving accuracy and resolving repetitive regions in synthetic constructs.

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

The paper develops crop-specific Nanopore basecalling models for Rosaceae species to improve sequencing quality and enables community use of these models.

Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

Emergence of short-lived meningococci causing focal epidemics can be associated with gene transfer from carriage-associated Neisseria

A 21-case nightclub-linked meningococcal outbreak variant differed from its closest relatives by horizontal gene transfer from carriage-associated Neisseria, affecting iron acquisition and type IV pili genes.

SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples

SVPG improves structural variant detection using pangenome references and accelerates pangenome graph construction from long-read data.

Somatic haplotype reconstruction and variant recalibration from tumor-only long-read sequencing

LongPhase-TO reconstructs somatic haplotypes from tumor-only long-read sequencing, improving variant calling accuracy and haplotype block size.

An Integrated Cell Culture - Nanopore Sequencing (ICC-NanoporeSeq) method for the simultaneous detection of multiple enterovirus types and quantification of infectious Enterovirus B

The paper develops ICC-NanoporeSeq to detect and quantify infectious Enterovirus B types in environmental samples, enabling type-resolved infectivity assessment.